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Identifier Type Title Topic Level Length
GTN:N00063 News Feedback: Easy slide recordings
feedbacktestimonialgtn
GTN:N00062 News GTN has left Twitter/X as of October
gtncommunications
GTN:N00061 News Update: Workflow List now searches WorkflowHub.eu, advanced query syntax
feature updategtn
GTN:N00060 News Single cell subdomain re-launch: Unified and feedback-driven
gtnsinglecell
GTN:N00059 News New Feature: Embeddable GTN Tutorial Lists and UseGalaxy Workflow List Widgets
new featuregtn
GTN:N00058 News New Feature: GTN User Preferences
new featuregtn
GTN:N00057 News AI4Life teams up with GTN to enhance training resources
new topicnew community
GTN:N00056 News ELIXIR-UK Fellow Launches New FAIR Data Management Training
new topicnew tutorial
GTN:N00055 News New Feature: Pan-Galactic Tool Search
new featuregtn
GTN:N00054 News GTN Celebrates Pride Month: Alan Hart & M. Tuberculosis
GTN:N00053 News New Galaxy training: Genome-wide alternative splicing analysis
new tutorial
GTN:N00052 News BY-COVID and RO-Crate collaboration brings new topic: FAIR Data, Workflows & More
new topicnew feature
GTN:N00051 News New Feature: my.galaxy.training
new featuregtn
GTN:N00050 News New Feature: Persistent URLs (PURLs) / Shortlinks
new featuregtn
GTN:N00049 News New Feature: GTN Rdoc
new featuregtn
GTN:N00048 News New Feature: Click-to-run Workflows
new featuregtn
GTN:N00047 News New Feature: Learning Pathways!
new feature
GTN:N00046 News New Feature: Trainer Directory! (Add yourself today!)
new featurecommunity buildingcapacity building
GTN:N00045 News What are the most used tools in the GTN?
new featuregtn
GTN:N00044 News GTN Celebrates Black History Month
GTN:N00043 News New Tutorial: Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
new tutorial
GTN:N00042 News New Feature: Prometheus Metrics endpoint
new featuregtn
GTN:N00041 News New GTN Feature Tag-based Topics enables new SARS-CoV-2 topic
new topicnew feature
GTN:N00040 News New GTN paper: "Galaxy Training: A powerful framework for teaching!"
paper
GTN:N00039 News New Tutorial Suite: Deconvolution with MuSiC, from public data to disease interrogation!
new tutorialsingle-celltranscriptomics
GTN:N00038 News New Topic: Single Cell Analysis!
new topicsingle-cellnew feature
GTN:N00037 News New Tutorial: Data Manipulation
new tutorial
GTN:N00036 News New Tutorial: Workflow Reports
new tutorialGalaxy Tips & Tricks
GTN:N00035 News GTN Metadata Schemas
new feature
GTN:N00034 News New Tutorial Feature: Choose Your Own Tutorial
gtn infrastructurenew featuretutorial authors
GTN:N00033 News New Tutorial: VGP assembly pipeline
new tutorialassemblypacbiovgp
GTN:N00032 News New Feature: Automatic RMarkdown
gtn infrastructurenew feature
GTN:N00031 News GTN Smörgåsbord 2: Tapas Edition
event
GTN:N00030 News Support for annotating Funding Agencies
new-feature
GTN:N00029 News New Tutorials: PacBio data QC and Genome Assembly, and Genome Annotation with Funannotate
new tutorialassemblygenome-annotation
GTN:N00028 News New FAQs: How does the GTN stay FAIR and Collaborative
faq
GTN:N00027 News New Feature: GTN Video Library
gtn infrastructurenew feature
GTN:N00026 News New Feature: GTN API with OpenAPI 3 specification
gtn infrastructurenew feature
GTN:N00025 News Attention Contributors: GTN Performance Enhancements
authorsdevelopersperformance
GTN:N00024 News New Topic: Data Science Survival Kit
gtn infrastructurenew topic
GTN:N00023 News Got a minute? Take our survey about Galaxy for training and have your say!
feedback
GTN:N00022 News New Feature: Automatic Jupyter Notebooks
gtn infrastructurenew feature
GTN:N00021 News New Feature: a feedback page to aggregate and display feedback answers
new featurecontributors
GTN:N00020 News Accessibility Improvements
new feature
GTN:N00019 News New Tutorial: Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
new tutorialvariant-analysiscovid-19
GTN:N00018 News New Tutorial: Visualization of RNA-Seq results with Volcano Plot in R
new tutorialvisualization
GTN:N00017 News New Tutorial: GitPod for contributing to the GTN
new tutorialcontributors
GTN:N00016 News New Tutorial: Genome Annotation with Apollo
new tutorialgenome-annotation
GTN:N00015 News Oh no, it changed! Quick, to the archive menu.
new feature
GTN:N00014 News Contributing to BioBlend as a developer
new tutorial
GTN:N00013 News New Feature: Easy Abbreviation
new feature
GTN:N00012 News ¿Hablas español?: The first curated tutorial in Spanish!
new tutorialespañol
GTN:N00011 News New Tutorials: Whole transcriptome analysis of Arabidopsis thaliana
new tutorialtranscriptomicsplantsmirna
GTN:N00010 News New Feature: Video Player
gtn infrastructurevideonew feature
GTN:N00009 News New Tutorial: Downstream Single-cell RNA Plant analysis with ScanPy
new tutorialsingle-cellplant
GTN:N00008 News New Tutorials: Genome assembly of a MRSA genome
new tutorialassemblymrsaamrnanoporeillumina
GTN:N00007 News New Feature: FAQs
gtn infrastructurecontributorsinstructorsnew feature
GTN:N00006 News New Tutorial: Object tracking using CellProfiler
new tutorialimaging
GTN:N00005 News Next GTN CoFest May 20, 2021
cofest
GTN:N00004 News Galaxy Community Conference 2021
event
GTN:N00003 News Report on the GTN Smörgåsbord event
eventpandemicremote-teaching
GTN:N00002 News Galaxy 21.01 released!
galaxy
GTN:N00001 News New Feature: Automatic Slides-to-video conversion
new featurevideosgtnpandemicremote-teaching
GTN:N00000 News Galaxy Admin Training Success
admingateventpandemicremote-teaching
GTN:F00282 FAQs Do I need to create collections to run MaxQuant analysis or can I use single sample inputs?
 Proteomics
GTN:F00283 FAQs Including custom modifications into MaxQuant in Galaxy?
 Proteomics
GTN:F00284 FAQs Which isobaric labeled quantification methods does MaxQuant in Galaxy support?
 Proteomics
GTN:F00137 FAQs How does the GTN ensure accessibility?
GTN:F00002 FAQs How do I create an account on a public Galaxy instance?
GTN:F00253 FAQs It says I already have an account when registering for ecology.usegalaxy.eu
 Ecology
GTN:F00003 FAQs Can I create multiple Galaxy accounts?
GTN:F00004 FAQs How can I reduce quota usage while still retaining prior work (data, tools, methods)?
GTN:F00005 FAQs How to update account preferences?
GTN:F00254 FAQs Automatically trim adapters (without providing custom sequences)
 Epigenetics
GTN:F00274 FAQs How can I adapt this tutorial to my own data?
 Metagenomics
GTN:F00271 FAQs How can I adapt this tutorial to my own data?
 Metagenomics
GTN:F00184 FAQs Operating system compatibility
 Galaxy Server administration
GTN:P00000 Admin Training Course
Galaxy administrators5-day course
GTN:F00280 FAQs What advantages does a Chromatogram Library have over a DDA-generated library or predicted spectral library?
 Proteomics
GTN:F00321 FAQs Why is Alevin is not working?
 Single Cell
GTN:F00320 FAQs Why is Alevin is not working?
 Single Cell
GTN:F00306 FAQs Is it possible to replace the existing alignment tools such as HISAT and Freebayes with other tools?
 Proteomics
GTN:F00234 FAQs Is it possible to use alternative tools to those proposed in the tutorial?
 Assembly
GTN:F00225 FAQs Why is amplification more of an issue in scRNA-seq than RNA-seq?
 Single Cell
GTN:F00006 FAQs Adding a custom database/build (dbkey)
GTN:F00174 FAQs Pick the right Concatenate tool
GTN:F00007 FAQs Beware of Cuts
GTN:F00008 FAQs Extended Help for Differential Expression Analysis Tools
GTN:F00009 FAQs Will my jobs keep running?
GTN:F00010 FAQs My jobs aren't running!
GTN:F00011 FAQs Regular Expressions 101
GTN:F00012 FAQs Reporting usage problems, security issues, and bugs
GTN:F00013 FAQs Results may vary
GTN:F00014 FAQs Troubleshooting errors
GTN:F00015 FAQs What information should I include when reporting a problem?
GTN:F00216 FAQs I can’t find the “Analyze Data” button
 Introduction to Galaxy Analyses
GTN:F00325 FAQs AnnData Import/ AnnData Manipulate not working?
 Single Cell
GTN:F00185 FAQs Variable connection
 Galaxy Server administration
GTN:F00186 FAQs Define once, reference many times
 Galaxy Server administration
GTN:F00187 FAQs What if you forget `--diff`?
 Galaxy Server administration
GTN:F00188 FAQs Error: "skipping: no hosts matched"
 Galaxy Server administration
GTN:F00189 FAQs Running Ansible on your remote machine
 Galaxy Server administration
GTN:F00190 FAQs What is the difference between the roles with `role:` prefix and without?
 Galaxy Server administration
GTN:F00191 FAQs How do I know what I can do with a role? What variables are available?
 Galaxy Server administration
GTN:F00192 FAQs How do I see what variables are set for a host?
 Galaxy Server administration
GTN:F00193 FAQs Is YAML sensitive to True/true/False/false
 Galaxy Server administration
GTN:F00236 FAQs Why does my assembly graph in Bandage look different to the one pictured in the tutorial?
 Assembly
GTN:F00243 FAQs The folder `recipes/belerophon/` and the file `meta.yaml` already exist in bioconda?
 Development in Galaxy
GTN:F00255 FAQs In bowtie 2 parameters, in place of 1000 for other experiments, should we mention the median fragment length observed in our library?
 Epigenetics
GTN:F00285 FAQs What is the advantage of breaking down protein to peptides before mass spec?
 Proteomics
GTN:F00277 FAQs The Build tissue-specific expression dataset tool (step one) exits with an error code.
 Proteomics
GTN:F00194 FAQs Opening a split screen in byobu
 Galaxy Server administration
GTN:F00307 FAQs Why do we change the chromosome names in the Ensembl GTF to match the UCSC genome reference?
 Proteomics
GTN:P00001 Discovering galaxy through climate analysis
ClimateOverview
GTN:F00259 FAQs Do you have resources to help me get started working in the cloud?
 Using Galaxy and Managing your Data
GTN:F00138 FAQs How does the GTN implement the "Ten simple rules for collaborative lesson development"
GTN:F00016 FAQs Adding a tag to a collection
GTN:F00017 FAQs Creating a dataset collection
GTN:F00018 FAQs Creating a paired collection
GTN:F00182 FAQs Changing the datatype of a collection
GTN:F00183 FAQs Converting the datatype of a collection
GTN:F00019 FAQs Renaming a collection
GTN:F00245 FAQs I want to use a collection for outputs but it always passes the test even when the script fails. Why?
 Development in Galaxy
GTN:F00296 FAQs How does one compare metaproteomics measurements from two experimental conditions?
 Proteomics
GTN:F00341 FAQs After sequencing with MinKNOW software, we get many fastq files, do these files need to be combined into one file before uploading or is it possible to upload them all at once?
 Metagenomics
GTN:F00286 FAQs Do we need a contaminant FASTA for MQ in galaxy?
 Proteomics
GTN:F00214 FAQs How to Contribute to Galaxy
 Development in Galaxy
GTN:F00212 FAQs Contributing a Jupyter Notebook to the GTN
 Contributing to the Galaxy Training Material
GTN:F00139 FAQs Thanks!
GTN:F00140 FAQs How can I get started with contributing?
GTN:F00141 FAQs How can I contribute in "advanced" mode?
GTN:F00142 FAQs How can I fix mistakes or expand an existing tutorial using the GitHub interface?
GTN:F00143 FAQs How can I give feedback?
GTN:F00144 FAQs What can I do to help the project?
GTN:F00145 FAQs How can I report mistakes or errors?
GTN:F00146 FAQs How can I test an Interactive Tour?
GTN:F00147 FAQs How can I create new content without dealing with git?
GTN:F00297 FAQs How does one convert RAW files to MGF peak lists within Galaxy?
 Proteomics
GTN:F00298 FAQs I have FASTQ files from metagenomics or metatranscriptomics datasets? How can I convert them into a protein FASTA file for metaproteomics searches?
 Proteomics
GTN:F00233 FAQs Customising the welcome page
 Galaxy Server administration
GTN:F00195 FAQs Database Issues
 Galaxy Server administration
GTN:F00020 FAQs Incomplete Dataset Download
GTN:F00021 FAQs How to find and correct tool errors related to Metadata?
GTN:F00023 FAQs Finding BAM dataset identifiers
GTN:F00024 FAQs Directly obtaining UCSC sourced *genome* identifiers
GTN:F00025 FAQs Adding a tag
GTN:F00177 FAQs Changer le type de données
GTN:F00026 FAQs Changing the datatype
GTN:F00128 FAQs Cambiar el tipo de datos
GTN:F00027 FAQs Changing database/build (dbkey)
GTN:F00028 FAQs Mismatched Chromosome identifiers and how to avoid them
GTN:F00029 FAQs Converting the file format
GTN:F00030 FAQs Creating a new file
GTN:F00031 FAQs How to set Data Privacy Features?
GTN:F00032 FAQs Detecting the datatype (file format)
GTN:F00033 FAQs Downloading datasets
GTN:F00034 FAQs Downloading datasets using command line
GTN:F00035 FAQs Finding Datasets
GTN:F00036 FAQs How to unhide "hidden datasets"?
GTN:F00037 FAQs Different dataset icons and their usage
GTN:F00038 FAQs Importing data from a data library
GTN:F00039 FAQs Importing data from remote files
GTN:F00040 FAQs Importing via links
GTN:F00129 FAQs Importación por medio de enlaces
GTN:F00178 FAQs Importer via un lien
GTN:F00041 FAQs Understanding job statuses
GTN:F00042 FAQs Moving datasets between Galaxy servers
GTN:F00043 FAQs Datasets not downloading at all
GTN:F00044 FAQs Purging datasets
GTN:F00045 FAQs Quotas for datasets and histories
GTN:F00046 FAQs Renaming a dataset
GTN:F00047 FAQs Upload few files (1-10)
GTN:F00048 FAQs Upload many files (>10) via FTP
GTN:F00049 FAQs Working with deleted datasets
GTN:F00050 FAQs Working with very large fasta datasets
GTN:F00051 FAQs Working with very large fastq datasets
GTN:F00052 FAQs Working with GFF GFT GTF2 GFF3 reference annotation
GTN:F00053 FAQs Using compressed fastq data as tool inputs
GTN:F00054 FAQs Best practices for loading fastq data into Galaxy
GTN:F00055 FAQs How do `fastq.gz` datasets relate to the `.fastqsanger` datatype metadata assignment?
GTN:F00056 FAQs Compressed FASTQ files, (`*.gz`)
GTN:F00057 FAQs How to format fastq data for tools that require .fastqsanger format?
GTN:F00058 FAQs FASTQ files: `fastq` vs `fastqsanger` vs ..
GTN:F00059 FAQs Identifying and formatting Tabular Datasets
GTN:F00060 FAQs Understanding Datatypes
GTN:F00061 FAQs How can I upload data using EBI-SRA?
GTN:F00062 FAQs Data retrieval with “NCBI SRA Tools” (fastq-dump)
GTN:F00063 FAQs NCBI SRA sourced fastq data
GTN:F00333 FAQs The tutorial uses the normalised count table for visualisation. What about using VST normalised counts or rlog normalised counts?
 Transcriptomics
GTN:F00299 FAQs What software tools are available to determine taxonomic composition from mass spectrometry data?
 Proteomics
GTN:F00331 FAQs Could I use a different p-adj value for filtering differentially expressed genes?
 Transcriptomics
GTN:F00329 FAQs I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why?
 Transcriptomics
GTN:F00196 FAQs How to read a Diff
 Galaxy Server administration
GTN:F00226 FAQs Why do we do dimension reduction and then clustering? Why not just cluster on the actual data?
 Single Cell
GTN:F00278 FAQs What is the principle of an enrichment analysis?
 Proteomics
GTN:F00246 FAQs My Rscript tool generates a strange R error on STDOUT about an invalid operation on a closure called 'args' ?
 Development in Galaxy
GTN:F00247 FAQs `docker-compose up` fails with error `/usr/bin/start.sh: line 133: /galaxy/.venv/bin/uwsgi: No such file or directory`
 Development in Galaxy
GTN:F00260 FAQs Where can I find example queries for use in the cloud and elsewhere?
 Using Galaxy and Managing your Data
GTN:F00148 FAQs How does the GTN ensure our training materials are FAIR?
GTN:F00224 FAQs FASTQ format
 Sequence analysis
GTN:F00267 FAQs Why do we use FASTQ interlacer and not the FASTQ joiner?
 Metagenomics
GTN:F00064 FAQs Using the Scratchbook to view multiple datasets
GTN:F00130 FAQs Uso del cuaderno de apuntes para ver varios conjuntos de datos
GTN:F00217 FAQs UCSC - I fetched data from a remote website but now I’m logged out of Galaxy and my data is gone?
 Introduction to Galaxy Analyses
GTN:F00322 FAQs My Scanpy FindMarkers step is giving me an empty table
 Single Cell
GTN:F00215 FAQs Flatten a list of list of paired datasets into a list of paired datasets
 Using Galaxy and Managing your Data
GTN:F00248 FAQs What file/data formats are defined for I/O in Galaxy?
 Development in Galaxy
GTN:F00300 FAQs Why do we do dimension reduction and then clustering? Why not just cluster on the actual data?
 Proteomics
GTN:F00317 FAQs Where can I read more about Quality Control of data?
 Sequence analysis
GTN:F00197 FAQs Blank page or no CSS/JavaScript
 Galaxy Server administration
GTN:F00198 FAQs How many mules?
 Galaxy Server administration
GTN:F00199 FAQs Debugging tool errors
 Galaxy Server administration
GTN:F00200 FAQs Debugging tool memory errors
 Galaxy Server administration
GTN:F00201 FAQs Tool missing from Galaxy
 Galaxy Server administration
GTN:F00202 FAQs Galaxy UI is slow
 Galaxy Server administration
GTN:F00357 FAQs Updating from 22.01 to 23.0 with Ansible
 Galaxy Server administration
GTN:F00218 FAQs My Galaxy looks different than in the tutorial/video
 Introduction to Galaxy Analyses
GTN:F00149 FAQs Are there any upcoming events focused on Galaxy Training?
GTN:F00180 FAQs Compatible Versions of Galaxy
GTN:F00150 FAQs Ways to use Galaxy
GTN:F00151 FAQs What is Galaxy?
GTN:F00279 FAQs What is Gene Ontology (GO)?
 Proteomics
GTN:F00227 FAQs What exactly is a ‘Gene profile’?
 Single Cell
GTN:P00002 Genome annotation for eukaryotes
genome annotationeukaryote
GTN:P00003 Genome annotation for prokaryotes
genome annotationprokaryote
GTN:F00152 FAQs How can I load data?
GTN:F00244 FAQs Where can I get planemo?
 Development in Galaxy
GTN:F00203 FAQs Using Git With Ansible Vaults
 Galaxy Server administration
GTN:F00204 FAQs Time to git commit
 Galaxy Server administration
GTN:F00205 FAQs Galaxy Admin Training Path
 Galaxy Server administration
GTN:F00153 FAQs What is this website?
GTN:F00154 FAQs How can I advertise the training materials on my posters?
GTN:F00155 FAQs What audiences are the tutorials for?
GTN:F00156 FAQs How can I cite the GTN?
GTN:F00157 FAQs How is the content licensed?
GTN:F00352 FAQs What licenses are used in the GTN?
GTN:F00158 FAQs Creating a GTN News post
GTN:F00159 FAQs GTN Stats
GTN:F00160 FAQs Sustainability of the training-material and metadata
GTN:F00161 FAQs What are the tutorials for?
GTN:F00162 FAQs Adding workflow tests with Planemo
GTN:F00256 FAQs Changing the heatmap colours
 Epigenetics
GTN:F00065 FAQs Copy a dataset between histories
GTN:F00179 FAQs Créer un nouvel history
GTN:F00066 FAQs Creating a new history
GTN:F00131 FAQs Para la creación de un historial nuevo
GTN:F00067 FAQs Downloading histories
GTN:F00068 FAQs Find all Histories and purge (aka permanently delete)
GTN:F00069 FAQs Finding Histories
GTN:F00070 FAQs Importing a history
GTN:F00071 FAQs Renaming a history
GTN:F00132 FAQs Cambiando el nombre de un historial
GTN:F00072 FAQs Searching your history
GTN:F00073 FAQs Finding and working with "Histories shared with me"
GTN:F00074 FAQs Sharing your History
GTN:F00133 FAQs Compartiendo un historial
GTN:F00075 FAQs Transfer entire histories from one Galaxy server to another
GTN:F00076 FAQs Undeleting history
GTN:F00077 FAQs Unsharing unwanted histories
GTN:F00342 FAQs What does `^.*Gallus|Homo|Bos.*$` mean?
 Metagenomics
GTN:F00343 FAQs For preprocessing part with host removal: Where do you find the abbreviations for each host species available (e.g. bos is cow, homo is human..)?
 Metagenomics
GTN:F00211 FAQs Most tools seem to have options for assembly using long and short reads, what are the pros and cons of the different tools?
 Assembly
GTN:F00239 FAQs Which icons are available to use in my tutorial?
 Contributing to the Galaxy Training Material
GTN:F00344 FAQs From where can I import other genomes?
 Metagenomics
GTN:F00334 FAQs When is the "infer experiment" tool used in practice?
 Transcriptomics
GTN:F00275 FAQs The input for a tool is not listed in the dropdown
 Metagenomics
GTN:F00272 FAQs The input for a tool is not listed in the dropdown
 Metagenomics
GTN:F00206 FAQs Install tools via the Admin UI
 Galaxy Server administration
GTN:F00164 FAQs What are the best practices for teaching with Galaxy?
GTN:F00165 FAQs What Galaxy instance should I use for my training?
GTN:F00166 FAQs How do I get help?
GTN:F00167 FAQs Where do I start?
GTN:F00079 FAQs Launch JupyterLab
GTN:F00080 FAQs Open a Terminal in Jupyter
GTN:F00081 FAQs Open interactive tool
GTN:F00082 FAQs Knitting RMarkdown documents in RStudio
GTN:F00083 FAQs Launch RStudio
GTN:F00084 FAQs Learning with RMarkdown in RStudio
GTN:F00085 FAQs Stop RStudio
GTN:P00004 Introduction to Galaxy and Ecological data analysis
beginner
GTN:P00005 Introduction to Galaxy and Sequence analysis
beginner
GTN:P00006 From R to Machine Learning; an introductory course
beginner
GTN:P00007 Introduction to Galaxy and Single Cell RNA Sequence analysis
beginner
GTN:P00012 Gallantries Grant - Intellectual Output 1 - Introduction to data analysis and -management, statistics, and coding
beginner
GTN:P00013 Gallantries Grant - Intellectual Output 2 - Large-scale data analysis, and introduction to visualisation and data modelling
beginner
GTN:P00014 Gallantries Grant - Intellectual Output 3 - Data stewardship, federation, standardisation, and collaboration
beginner
GTN:P00015 Gallantries Grant - Intellectual Output 4 - Data analysis and modelling for evidence and hypothesis generation and knowledge discovery
beginner
GTN:P00016 Gallantries Grant - Intellectual Output 5 - Train-the-Trainer and mentoring programme
beginner
GTN:F00168 FAQs What information should I include when reporting a problem?
GTN:F00315 FAQs JBrowse is taking a long time to complete?
 Sequence analysis
GTN:F00249 FAQs First job I submitted remains grey or running for a long time - is it broken?
 Development in Galaxy
GTN:F00345 FAQs Is there a way to filter on the Kalimari database?
 Metagenomics
GTN:F00338 FAQs TB Variant Report crashes (with an error about KeyError: 'protein')
 Variant Analysis
GTN:F00221 FAQs Kraken2 and the k-mer approach for taxonomy classification
 Metagenomics
GTN:F00169 FAQs How can I get help?
GTN:F00170 FAQs Where do I start?
GTN:F00171 FAQs Where can I run the hands-on tutorials?
GTN:F00172 FAQs How do I use this material?
GTN:F00213 FAQs Defining a Learning Pathway
 Contributing to the Galaxy Training Material
GTN:F00207 FAQs Library Permission Issues
 Galaxy Server administration
GTN:F00250 FAQs Why do I need that big (~5GB!) complicated Docker thing - can I just install the ToolFactory into our local galaxy server from the toolshed?
 Development in Galaxy
GTN:F00219 FAQs My jobs are not running / I cannot see the history overview menu
 Introduction to Galaxy Analyses
GTN:F00208 FAQs Failing all jobs from a specific user
 Galaxy Server administration
GTN:F00209 FAQs Mapping Jobs to Specific Storage By User
 Galaxy Server administration
GTN:F00287 FAQs When can you use (or cannot use) Match between runs in MaxQuant?
 Proteomics
GTN:F00288 FAQs Do you need to merge the databases? Because you can select multiple fasta files in MaxQuant.
 Proteomics
GTN:F00261 FAQs Where can I find the full listing and description of the columns in each metadata table?
 Using Galaxy and Managing your Data
GTN:P00008 Metagenomics data processing and analysis for microbiome
microbiome
GTN:F00210 FAQs Got lost along the way?
 Galaxy Server administration
GTN:F00276 FAQs Where can I read more about this analysis?
 Metagenomics
GTN:F00273 FAQs Where can I read more about this analysis?
 Metagenomics
GTN:F00289 FAQs If you use a mqpar file, can you include modifications that are not in the Galaxy version? For instance, propionamide (Cys alkylation by acrylamide).
 Proteomics
GTN:F00268 FAQs Can we use the ASaiM-MT workflow on multiple input files at the same time?
 Metagenomics
GTN:F00318 FAQs MultiQC error for your FastQC reports?
 Sequence analysis
GTN:F00313 FAQs In the MVP platform, is it possible to view the genomic location of all the peptides?
 Proteomics
GTN:F00241 FAQs I cannot run client tests because yarn is not installed.
 Development in Galaxy
GTN:F00290 FAQs What does it mean to normalize the LFQ intensities?
 Proteomics
GTN:F00355 FAQs Notebook-based tutorials can give different outputs
 Single Cell
GTN:F00262 FAQs When will aligned read objects be available for other data types?
 Using Galaxy and Managing your Data
GTN:F00291 FAQs Does MaxQuant give as output possibility the PSMs and PEPs?
 Proteomics
GTN:F00319 FAQs When I get a warning for base per sequence content, what should I do?
 Sequence analysis
GTN:F00237 FAQs Running more than one round of Pilon polishing
 Assembly
GTN:F00251 FAQs Only one Planemo test runs at a time. Why doesn't the server allow more than one at once?
 Development in Galaxy
GTN:F00323 FAQs On Scanpy PlotEmbed, the tool is failing
 Single Cell
GTN:F00324 FAQs On the Scanpy PlotEmbed step, my object doesn’t have Il2ra or Cd8b1 or Cd8a etc.
 Single Cell
GTN:F00238 FAQs Can we polish the assembly with long reads too?
 Assembly
GTN:F00086 FAQs Getting your API key
GTN:F00308 FAQs Example histories for the proteogenomics tutorials
 Proteomics
GTN:F00309 FAQs Can I use these workflows on datasets generated from our laboratory?
 Proteomics
GTN:F00310 FAQs The workflows contain several Query tabular for text manipulation, is there a tutorial for that?
 Proteomics
GTN:F00311 FAQs What kind of variants are seen in the output?
 Proteomics
GTN:F00327 FAQs How do I know what protocol my data was sequenced with?
 Single Cell
GTN:F00351 FAQs Debugging Memory Leaks
 Galaxy Server administration
GTN:P00009 Introductory Python
pythonreal-course
GTN:F00263 FAQs Why don't the aligned read files have quality scores?
 Using Galaxy and Managing your Data
GTN:F00350 FAQs Quality Scores
 Sequence analysis
GTN:F00332 FAQs Can I use alternative tools for the Quantification step?
 Transcriptomics
GTN:F00292 FAQs For the “quantitation method” what is the default if I just leave it as “None”? Label free?
 Proteomics
GTN:F00266 FAQs Why does the query `SRR11772204 OR SRR11597145 OR SRR11667145` in the Run Selector not return any results?
 Introduction to Galaxy Analyses
GTN:F00328 FAQs Are Barcodes always on R1 and Sequence data on R2?
 Single Cell
GTN:F00087 FAQs How to use Custom Reference Genomes?
GTN:F00088 FAQs Sorting Reference Genome
GTN:F00089 FAQs Troubleshooting Custom Genome fasta
GTN:F00346 FAQs Isn't it awkward to find so many humans sequences there, since we filter for them before?
 Metagenomics
GTN:F00358 FAQs Preparing materials for asynchronous learning: CYOA
 Contributing to the Galaxy Training Material
GTN:F00359 FAQs Preparing materials for asynchronous learning: FAQs
 Contributing to the Galaxy Training Material
GTN:F00360 FAQs Preparing materials for asynchronous learning: Self-Study
 Contributing to the Galaxy Training Material
GTN:F00361 FAQs Preparing materials for asynchronous learning: Tips
 Contributing to the Galaxy Training Material
GTN:F00252 FAQs Is the ToolFactory a complete replacement for manual tool building?
 Development in Galaxy
GTN:F00223 FAQs Additional resources to learn more about proteomic data analysis
 Proteomics
GTN:F00301 FAQs Can I use these workflows on datasets generated from our laboratory?
 Proteomics
GTN:F00335 FAQs Is it possible to visualize the RNA STAR bam file using the JBrowse tool?
 Transcriptomics
GTN:F00336 FAQs RNAstar: Why do we set 36 for 'Length of the genomic sequence around annotated junctions'?
 Transcriptomics
GTN:F00339 FAQs My snippy is running for a very long time. Is this normal?
 Variant Analysis
GTN:F00265 FAQs What should I do special if on usegalaxy.be?
 Using Galaxy and Managing your Data
GTN:F00302 FAQs Which search algorithms are recommended for searching the metaproteomics data?
 Proteomics
GTN:F00314 FAQs How many search engines can you use in SearchGUI?
 Proteomics
GTN:F00303 FAQs I have a really large search database, what search strategies do you recommend for searching my mass spectrometry dataset?
 Proteomics
GTN:F00242 FAQs When I try to run a Selenium test, I get an error
 Development in Galaxy
GTN:F00090 FAQs Illumina MiSeq sequencing
GTN:F00091 FAQs Nanopore sequencing
GTN:F00293 FAQs How many proteins can be identified and quantified in shotgun proteomics?
 Proteomics
GTN:F00353 FAQs Use our single cell Galaxy instance
 Single Cell
GTN:F00269 FAQs Can this ASaiM workflow be used for single-end data?
 Metagenomics
GTN:S00080 Slides Introduction to proteomics, protein identification, quantification and statistical modelling
 Proteomics
GTN:S00039 Slides The Pangeo ecosystem
climate		 Climate 15m
GTN:S00036 Slides Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
climateecology		 Climate 30m
GTN:S00037 Slides Introduction to climate data
 Climate
GTN:S00038 Slides Pangeo ecosystem 101 for everyone
climate		 Climate 15m
GTN:S00042 Slides Overview of the Galaxy Training Material
 Contributing to the Galaxy Training Material
GTN:S00040 Slides Creating Slides
 Contributing to the Galaxy Training Material
GTN:S00041 Slides Contributing with GitHub via command-line
 Contributing to the Galaxy Training Material 30m
GTN:S00099 Slides Introduction to Variant analysis
 Variant Analysis
GTN:S00060 Slides Introduction to DNA Methylation data analysis
 Epigenetics
GTN:S00058 Slides ChIP-seq data analysis
 Epigenetics 15M
GTN:S00057 Slides EWAS Epigenome-Wide Association Studies Introduction
 Epigenetics
GTN:S00059 Slides Introduction to ChIP-Seq data analysis
 Epigenetics
GTN:S00056 Slides Introduction to ATAC-Seq data analysis
 Epigenetics 30m
GTN:S00071 Slides Nucleoli Segmentation
&
Feature Extraction
using CellProfiler
 Imaging 4H
GTN:S00078 Slides Introduction to metagenomics
 Metagenomics
GTN:S00079 Slides Introduction to metatranscriptomics
 Metagenomics
GTN:S00101 Slides Visualisations in Galaxy
 Visualisation
GTN:S00112 Slides Friends Don't Let Friends Make Bad Graphs
 Visualisation
GTN:S00100 Slides Circos
 Visualisation
GTN:S00102 Slides JBrowse
 Visualisation
GTN:S00109 Slides Bioinformatics Data Types and Databases
 Foundations of Data Science 1h
GTN:S00047 Slides Tool Dependencies and Containers
 Development in Galaxy 45m
GTN:S00053 Slides Visualizations: JavaScript Plugins
 Development in Galaxy 1h
GTN:S00051 Slides Tool development and integration into Galaxy
 Development in Galaxy 6h
GTN:S00046 Slides Prerequisites for building software/conda packages
 Development in Galaxy 1h
GTN:S00049 Slides Galaxy Interactive Tours
 Development in Galaxy 3h
GTN:S00052 Slides Tool Shed: sharing Galaxy tools
 Development in Galaxy 3h
GTN:S00043 Slides Galaxy Code Architecture
 Development in Galaxy 150m
GTN:S00048 Slides Galaxy Interactive Environments
 Development in Galaxy 90m
GTN:S00045 Slides Tool Dependencies and Conda
 Development in Galaxy 75m
GTN:S00050 Slides Introduction to the ToolFactory tutorial.
 Development in Galaxy
GTN:S00054 Slides Generic plugins
 Development in Galaxy 90m
GTN:S00044 Slides Scripting Galaxy using the API and BioBlend
 Development in Galaxy 2h
GTN:S00055 Slides Galaxy Webhooks
 Development in Galaxy 1h
GTN:S00005 Slides Connecting Galaxy to a compute cluster
features		 Galaxy Server administration
GTN:S00024 Slides Terraform
 Galaxy Server administration
GTN:S00017 Slides Galaxy Monitoring with Telegraf and Grafana
 Galaxy Server administration
GTN:S00012 Slides Galaxy Monitoring
 Galaxy Server administration
GTN:S00002 Slides Galaxy Installation with Ansible
 Galaxy Server administration
GTN:S00008 Slides Galactic Database
 Galaxy Server administration
GTN:S00014 Slides Galaxy Interactive Tools
 Galaxy Server administration
GTN:S00020 Slides Running Jobs on Remote Resources with Pulsar
jobs		 Galaxy Server administration 60m
GTN:S00103 Slides Server Maintenance: Cleanup, Backup, and Restoration
 Galaxy Server administration 30m
GTN:S00004 Slides Galaxy on the Cloud
 Galaxy Server administration
GTN:S00025 Slides Galaxy Tool Management with Ephemeris
 Galaxy Server administration
GTN:S00015 Slides Galaxy from an administrator's point of view
 Galaxy Server administration 20m
GTN:S00028 Slides uWSGI
 Galaxy Server administration
GTN:S00022 Slides Server: Other
 Galaxy Server administration 1h
GTN:S00007 Slides Storage Management
 Galaxy Server administration
GTN:S00001 Slides Ansible
 Galaxy Server administration
GTN:S00026 Slides Galaxy Troubleshooting
 Galaxy Server administration
GTN:S00009 Slides Empathy
 Galaxy Server administration
GTN:S00003 Slides Galaxy and Celery
 Galaxy Server administration
GTN:S00027 Slides User, Role, Group, Quota, and Authentication managment
 Galaxy Server administration 15m
GTN:S00013 Slides Galaxy Monitoring with gxadmin
 Galaxy Server administration
GTN:S00011 Slides Docker and Galaxy
 Galaxy Server administration 1h
GTN:S00010 Slides External Authentication
 Galaxy Server administration
GTN:S00006 Slides Reference Data with CVMFS
 Galaxy Server administration
GTN:S00000 Slides Advanced customisation of a Galaxy instance
 Galaxy Server administration
GTN:S00019 Slides Gearing towards production
 Galaxy Server administration
GTN:S00018 Slides Storage Management
 Galaxy Server administration
GTN:S00023 Slides Controlling Galaxy with systemd or Supervisor
 Galaxy Server administration
GTN:S00021 Slides Reference Genomes in Galaxy
 Galaxy Server administration
GTN:S00082 Slides Quality Control
 Sequence analysis 1h
GTN:S00081 Slides Mapping
 Sequence analysis 1h
GTN:S00072 Slides A Short Introduction to Galaxy
 Introduction to Galaxy Analyses
GTN:S00073 Slides Introduction to Galaxy
 Introduction to Galaxy Analyses
GTN:S00075 Slides Options for using Galaxy
 Introduction to Galaxy Analyses
GTN:S00110 Slides Automated Cell Annotation
 Single Cell
GTN:S00085 Slides Plates, Batches, and Barcodes
 Single Cell 1h
GTN:S00087 Slides Clustering 3K PBMCs with Scanpy
 Single Cell 1H
GTN:S00084 Slides An introduction to scRNA-seq data analysis
 Single Cell Intermediate 30m
GTN:S00111 Slides Trajectory analysis
 Single Cell
GTN:S00086 Slides Dealing with Cross-Contamination in Fixed Barcode Protocols
 Single Cell 1h
GTN:S00092 Slides Overview of the Galaxy Training Material for Instructors
 Teaching and Hosting Galaxy training 10M
GTN:S00093 Slides Workshop Kickoff
 Teaching and Hosting Galaxy training 30m
GTN:S00035 Slides Unicycler Assembly
prokaryote		 Assembly 4h
GTN:S00034 Slides An introduction to get started in genome assembly and annotation
 Assembly Introductory 1h
GTN:S00031 Slides Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
covid19		 Assembly 4h
GTN:S00032 Slides De Bruijn Graph Assembly
 Assembly 2h
GTN:S00033 Slides An Introduction to Genome Assembly
 Assembly 30m
GTN:S00030 Slides Genome assembly quality control.
 Assembly Introductory
GTN:S00029 Slides Deeper look into Genome Assembly algorithms
 Assembly Intermediate
GTN:S00105 Slides BioImage Model Zoo: Advanced models in one-click
bioimageioimage analysis		 Image analysis using Deep Learning 5m
GTN:S00107 Slides Contribute to the BioImage.IO models
bioimageioimage analysis		 Image analysis using Deep Learning 10m
GTN:S00106 Slides Welcome to the BioImage Model Zoo
bioimageioimage analysis		 Image analysis using Deep Learning 5m
GTN:S00096 Slides Network Analysis with Heinz
 Transcriptomics
GTN:S00098 Slides Visualization of RNA-Seq results with CummeRbund
 Transcriptomics 1h
GTN:S00094 Slides Introduction to Transcriptomics
 Transcriptomics
GTN:S00108 Slides Identification of non-canonical ORFs and their potential biological function
 Transcriptomics
GTN:S00095 Slides Whole transcriptome analysis of Arabidopsis thaliana
 Transcriptomics
GTN:S00097 Slides Integrate and query local datasets and distant RDF data with AskOmics using Semantic Web technologies
 Transcriptomics
GTN:S00064 Slides Submitting SARS-CoV-2 sequences to ENA
 Using Galaxy and Managing your Data 1h
GTN:S00062 Slides Getting data into Galaxy
 Using Galaxy and Managing your Data
GTN:S00061 Slides Galaxy workflows in Dockstore
 Using Galaxy and Managing your Data
GTN:S00063 Slides Introduction to SRA Aligned Read Format and Cloud Metadata for SARS-CoV-2
ncbicovid19		 Using Galaxy and Managing your Data 10m
GTN:S00089 Slides Feedforward neural networks (FNN) Deep Learning - Part 1
 Statistics and machine learning
GTN:S00090 Slides Recurrent neural networks (RNN) Deep Learning - Part 2
 Statistics and machine learning
GTN:S00088 Slides Convolutional neural networks (CNN) Deep Learning - Part 3
 Statistics and machine learning
GTN:S00091 Slides Image classification in Galaxy with fruit 360 dataset
 Statistics and machine learning 2H
GTN:S00068 Slides High Performance Computing for Pairwise Genome Comparison
 Genome Annotation 2h
GTN:S00066 Slides Refining Genome Annotations with Apollo
prokaryote		 Genome Annotation 5m
GTN:S00069 Slides Introduction to Genome Annotation
 Genome Annotation Intermediate
GTN:S00067 Slides Introduction to CRISPR screen analysis
 Genome Annotation 5m
GTN:S00070 Slides Essential genes detection with Transposon insertion sequencing
bacteriatnseqessential genes		 Genome Annotation 7H
GTN:S00065 Slides Genome annotation with Prokka
prokaryote		 Genome Annotation 1h
GTN:S00076 Slides Introduction to Metabolomics
 Metabolomics
GTN:S00077 Slides Mass spectrometry: LC-MS preprocessing - advanced
 Metabolomics
GTN:F00316 FAQs What is a SNP?
 Sequence analysis
GTN:P00010 Introductory SQL
pythonreal-course
GTN:F00294 FAQs MSStats: what does ‘compare groups = yes’ mean? And the comparison matrix to define the contrast between the 2 groups?
 Proteomics
GTN:F00337 FAQs In 'infer experiments' I get unequal numbers, but in the IGV it looks like it is unstranded. What does this mean?
 Transcriptomics
GTN:F00304 FAQs What other methods are available to study the functional state of the microbiome within Galaxy?
 Proteomics
GTN:F00257 FAQs Is it possible to subsample some samples if you have more reads?
 Epigenetics
GTN:F00092 FAQs Where do I get more support?
GTN:F00093 FAQs Contacting Galaxy Administrators
GTN:F00222 FAQs What is Taxonomy?
 Metagenomics
GTN:F00228 FAQs Can RNA-seq techniques be applied to scRNA-seq?
 Single Cell
GTN:F00264 FAQs Are these data free to use and download?
 Using Galaxy and Managing your Data
GTN:F00295 FAQs Does MaxQuant in Galaxy support TMT, iTRAQ, etc.?
 Proteomics
GTN:F00340 FAQs Do I have to run the tools in the order of the tutorial?
 Variant Analysis
GTN:F00094 FAQs Changing the tool version
GTN:F00095 FAQs Organizing the tool panel
GTN:F00096 FAQs Where is the tool help?
GTN:F00097 FAQs Viewing tool logs (`stdout` and `stderr`)
GTN:F00098 FAQs If a Tool is Missing
GTN:F00099 FAQs Re-running a tool
GTN:F00135 FAQs Para volver a ejecutar una herramienta
GTN:F00100 FAQs Selecting a dataset collection as input
GTN:F00101 FAQs Select multiple datasets
GTN:F00102 FAQs Multipile similar tools available
GTN:F00103 FAQs Sorting Tools
GTN:F00104 FAQs Tool doesn't recognize input datasets
GTN:F00305 FAQs Which version of SearchGUI and PeptideShaker shall I use for this tutorial?
 Proteomics
GTN:P00011 Train the Trainers
trainingtrainers
GTN:F00330 FAQs I’m using the same training data, tools, and parameters as the tutorial, but I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why?
 Transcriptomics
GTN:F00105 FAQs Understanding 'canceled by admin' or cluster failure error messages
GTN:F00106 FAQs Understanding 'exceeds memory allocation' error messages
GTN:F00107 FAQs Understanding input error messages
GTN:F00108 FAQs Understanding ValueError error messages
GTN:F00109 FAQs Understanding walltime error messages
GTN:T00368 Hands-on Making clinical datasets FAIR
fairopendata stewardship		 FAIR Data, Workflows, and Research 1H
GTN:T00361 Hands-on REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data
fairdata managementbioimaging		 FAIR Data, Workflows, and Research 15m
GTN:T00369 Hands-on Sequence data submission to ENA
FAIRENA		 FAIR Data, Workflows, and Research 1H
GTN:T00362 Hands-on FAIR Bioimage Metadata
fairdata managementbioimaging		 FAIR Data, Workflows, and Research 15m
GTN:T00350 Hands-on FAIR Galaxy Training Material
fairgtntraining		 FAIR Data, Workflows, and Research 30M
GTN:T00339 Hands-on Best practices for workflows in GitHub repositories
ro-cratejupyter-notebook		 FAIR Data, Workflows, and Research 30M
GTN:T00343 Hands-on Workflow Run RO-Crate Introduction
ro-crate		 FAIR Data, Workflows, and Research 30M
GTN:T00341 Hands-on RO-Crate in Python
ro-cratejupyter-notebook		 FAIR Data, Workflows, and Research 30M
GTN:T00349 Hands-on FAIR data management solutions
fairdmpdata stewardship		 FAIR Data, Workflows, and Research 10M
GTN:T00348 Hands-on RO-Crate - Introduction
 FAIR Data, Workflows, and Research Introductory 30M
GTN:T00342 Hands-on Submitting workflows to LifeMonitor
ro-crate		 FAIR Data, Workflows, and Research 30M
GTN:T00340 Hands-on Exporting Workflow Run RO-Crates from Galaxy
ro-crateworkflows		 FAIR Data, Workflows, and Research 30m
GTN:T00351 Hands-on FAIR in a nutshell
fairopendata stewardship		 FAIR Data, Workflows, and Research 10M
GTN:T00216 Hands-on Label-free versus Labelled - How to Choose Your Quantitation Method
DDA		 Proteomics Introductory 15m
GTN:T00222 Hands-on metaQuantome 1: Data creation
microgalaxy		 Proteomics Intermediate 1h
GTN:T00215 Hands-on EncyclopeDIA
DIA		 Proteomics 6H
GTN:T00228 Hands-on Peptide and Protein ID using OpenMS tools
DDAHeLa		 Proteomics Advanced 45m
GTN:T00229 Hands-on Peptide and Protein ID using SearchGUI and PeptideShaker
DDAHeLa		 Proteomics Introductory 45m
GTN:T00220 Hands-on MaxQuant and MSstats for the analysis of TMT data
DDATMT		 Proteomics 3H
GTN:T00224 Hands-on metaQuantome 3: Taxonomy
microgalaxy		 Proteomics Intermediate 1h
GTN:T00214 Hands-on Protein FASTA Database Handling
DDA		 Proteomics Introductory 30m
GTN:T00233 Hands-on Proteogenomics 3: Novel peptide analysis
proteogenomics		 Proteomics Intermediate 30m
GTN:T00223 Hands-on metaQuantome 2: Function
microgalaxy		 Proteomics Intermediate 1h
GTN:T00231 Hands-on Proteogenomics 1: Database Creation
proteogenomics		 Proteomics Intermediate 30m
GTN:T00230 Hands-on Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
DDASILAC		 Proteomics Advanced 1h
GTN:T00235 Hands-on Secretome Prediction
humanwork-in-progress		 Proteomics Intermediate 30m
GTN:T00213 Hands-on Biomarker candidate identification
DDAhuman		 Proteomics 3H
GTN:T00217 Hands-on Mass spectrometry imaging: Loading and exploring MSI data
mouseimaging		 Proteomics Introductory 45m
GTN:T00212 Hands-on Library Generation for DIA Analysis
DIA		 Proteomics Intermediate 1H
GTN:T00221 Hands-on Metaproteomics tutorial
microgalaxy		 Proteomics 2h
GTN:T00211 Hands-on DIA Analysis using OpenSwathWorkflow
DIA		 Proteomics Intermediate 2H
GTN:T00234 Hands-on Annotating a protein list identified by LC-MS/MS experiments
DDAhuman		 Proteomics 1H
GTN:T00219 Hands-on MaxQuant and MSstats for the analysis of label-free data
label-free		 Proteomics Intermediate 2H
GTN:T00227 Hands-on Peptide Library Data Analysis
 Proteomics Intermediate 20m
GTN:T00210 Hands-on Statistical analysis of DIA data
DIA		 Proteomics Intermediate 1H
GTN:T00225 Hands-on Machine Learning Modeling of Anticancer Peptides
MLcancer		 Proteomics Intermediate 30m
GTN:T00232 Hands-on Proteogenomics 2: Database Search
proteogenomics		 Proteomics Intermediate 15m
GTN:T00226 Hands-on Detection and quantitation of N-termini (degradomics) via N-TAILS
 Proteomics Intermediate 1h
GTN:T00218 Hands-on Label-free data analysis using MaxQuant
DDAlabel-free		 Proteomics Introductory 1H
GTN:T00045 Hands-on Pangeo Notebook in Galaxy - Introduction to Xarray
pangeointeractive-toolsjupyter-notebook		 Climate 1H
GTN:T00043 Hands-on Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab
interactive-tools		 Climate 6H
GTN:T00041 Hands-on Getting your hands-on climate data
 Climate 1H
GTN:T00042 Hands-on Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
interactive-tools		 Climate 4H
GTN:T00046 Hands-on Visualize Climate data with Panoply netCDF viewer
interactive-tools		 Climate 1H
GTN:T00044 Hands-on Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools
pangeo		 Climate 1H
GTN:T00274 Hands-on Evaluating and ranking a set of pathways based on multiple metrics
 Synthetic Biology 20M
GTN:T00275 Hands-on Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
 Synthetic Biology 30M
GTN:T00273 Hands-on Designing plasmids encoding predicted pathways by using the BASIC assembly method
 Synthetic Biology 15M
GTN:T00063 Hands-on Generating PDF artefacts of the website
 Contributing to the Galaxy Training Material 10m
GTN:T00056 Hands-on Including a new topic
 Contributing to the Galaxy Training Material 30m
GTN:T00066 Hands-on Running the GTN website online using GitPod
 Contributing to the Galaxy Training Material 15m
GTN:T00363 Hands-on FAIR Galaxy Training Material
fairgtntraining		 Contributing to the Galaxy Training Material 30M
GTN:T00062 Hands-on Design and plan session, course, materials
 Contributing to the Galaxy Training Material 60m
GTN:T00058 Hands-on Creating content in Markdown
 Contributing to the Galaxy Training Material 15m
GTN:T00068 Hands-on Teaching Python
 Contributing to the Galaxy Training Material 2h
GTN:T00059 Hands-on Adding Quizzes to your Tutorial
 Contributing to the Galaxy Training Material 15m
GTN:T00071 Hands-on Adding auto-generated video to your slides
 Contributing to the Galaxy Training Material 20m
GTN:T00067 Hands-on Principles of learning and how they apply to training and teaching
 Contributing to the Galaxy Training Material 2h
GTN:T00070 Hands-on GTN Metadata
 Contributing to the Galaxy Training Material 10m
GTN:T00065 Hands-on Contributing with GitHub via its interface
 Contributing to the Galaxy Training Material 20m
GTN:T00055 Hands-on Updating diffs in admin training
 Contributing to the Galaxy Training Material 5m
GTN:T00069 Hands-on Running the GTN website locally
 Contributing to the Galaxy Training Material 15m
GTN:T00057 Hands-on Creating a new tutorial
 Contributing to the Galaxy Training Material 15m
GTN:T00060 Hands-on Tools, Data, and Workflows for tutorials
 Contributing to the Galaxy Training Material 30m
GTN:T00061 Hands-on Creating Interactive Galaxy Tours
 Contributing to the Galaxy Training Material 15m
GTN:T00064 Hands-on Contributing with GitHub via command-line
 Contributing to the Galaxy Training Material 30m
GTN:T00131 Hands-on Visualize EBV cube data with Panoply netCDF viewer
interactive-toolsEBV cubeData visualization		 Ecology 1H
GTN:T00126 Hands-on Biodiversity data exploration
taxonomic datadata quality		 Ecology 1H
GTN:T00132 Hands-on Preparing genomic data for phylogeny reconstruction
phylogenydata handlingfunctional annotation		 Ecology 3H
GTN:T00333 Hands-on Sentinel 2 biodiversity
Remote sensing		 Ecology 48H
GTN:T00125 Hands-on Compute and analyze biodiversity metrics with PAMPA toolsuite
Species population EBV classCommunity composition EBV classEBV datasetEBV workflowmodeling		 Ecology 2H
GTN:T00130 Hands-on RAD-Seq to construct genetic maps
RAD-seqGenetic composition EBV classEBV datasetEBV workflow		 Ecology 8h
GTN:T00134 Hands-on Regional GAM
Species populations EBV classSpecies traits EBV classEBV datasetEBV workflow		 Ecology 2h30m
GTN:T00367 Hands-on QGIS Web Feature Services
GISGeographical Information SystemWFSSpatial dataQGISMapsOGC		 Ecology 0H30M
GTN:T00124 Hands-on Metabarcoding/eDNA through Obitools
Genetic composition EBV classCommunity composition EBV classEBV datasetEBV workfloweDNAMetabarcoding		 Ecology 1H
GTN:T00127 Hands-on Champs blocs indicators
 Ecology 1H
GTN:T00128 Hands-on RAD-Seq de-novo data analysis
RAD-seqGenetic composition EBV classSpecies populations EBV classEBV datasetEBV workflow		 Ecology 8h
GTN:T00129 Hands-on Cleaning GBIF data for the use in Ecology
gbifdata managementdata cleaning		 Ecology 0H30M
GTN:T00332 Hands-on Obis marine indicators
 Ecology 1H
GTN:T00135 Hands-on Species distribution modeling
interactive-toolsmodelinggbifspecies populations EBV class		 Ecology 1h
GTN:T00133 Hands-on RAD-Seq Reference-based data analysis
RAD-seqGenetic composition EBV classSpecies population EBV classEBV datasetEBV workflow		 Ecology 8h
GTN:T00136 Hands-on Visualization of Climate Data using NetCDF xarray Map Plotting
pangeo		 Ecology Introductory 1H
GTN:T00314 Hands-on Calling variants in non-diploid systems
prokaryotemicrogalaxy		 Variant Analysis 1h30m
GTN:T00320 Hands-on Trio Analysis using Synthetic Datasets from RD-Connect GPAP
cyoa		 Variant Analysis 2H
GTN:T00317 Hands-on Somatic Variant Discovery from WES Data Using Control-FREEC
 Variant Analysis 3H
GTN:T00319 Hands-on M. tuberculosis Variant Analysis
prokaryoteone-healthmicrogalaxy		 Variant Analysis Intermediate 2h
GTN:T00318 Hands-on Identification of somatic and germline variants from tumor and normal sample pairs
 Variant Analysis 7h
GTN:T00347 Hands-on Pox virus genome analysis from tiled-amplicon sequencing data
virologyone-health		 Variant Analysis Advanced 4H
GTN:T00309 Hands-on Calling variants in diploid systems
 Variant Analysis 3h
GTN:T00310 Hands-on Calling very rare variants
 Variant Analysis 3h
GTN:T00312 Hands-on Mapping and molecular identification of phenotype-causing mutations
 Variant Analysis 2h
GTN:T00313 Hands-on Microbial Variant Calling
prokaryotemicrogalaxy		 Variant Analysis 45m
GTN:T00315 Hands-on From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
covid19virologyone-health		 Variant Analysis 1H
GTN:T00308 Hands-on Avian influenza viral strain analysis from gene segment sequencing data
virologyone-health		 Variant Analysis Intermediate 4H
GTN:T00316 Hands-on Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
covid19virologyone-health		 Variant Analysis Intermediate 3H
GTN:T00311 Hands-on Exome sequencing data analysis for diagnosing a genetic disease
 Variant Analysis 5h
GTN:T00138 Hands-on Identification of the binding sites of the Estrogen receptor
ChIP-seqwork-in-progress		 Epigenetics 3h
GTN:T00140 Hands-on Formation of the Super-Structures on the Inactive X
ChIP-seq		 Epigenetics 3h
GTN:T00143 Hands-on Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
ChIP-seq		 Epigenetics 3h
GTN:T00139 Hands-on Infinium Human Methylation BeadChip
 Epigenetics 1h
GTN:T00142 Hands-on DNA Methylation data analysis
 Epigenetics 3h
GTN:T00137 Hands-on ATAC-Seq data analysis
 Epigenetics 3h
GTN:T00141 Hands-on Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
 Epigenetics 1h
GTN:T00364 Hands-on REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data
fairdata managementbioimaging		 Imaging 15m
GTN:T00365 Hands-on FAIR Bioimage Metadata
fairdata managementbioimaging		 Imaging 15m
GTN:T00334 Hands-on End-to-End Tissue Microarray Image Analysis with Galaxy-ME
 Imaging 3H
GTN:T00180 Hands-on Analyse HeLa fluorescence siRNA screen
HeLa		 Imaging Intermediate 1H
GTN:T00182 Hands-on Object tracking using CellProfiler
 Imaging 1H
GTN:T00183 Hands-on Nucleoli segmentation and feature extraction using CellProfiler
 Imaging 4H
GTN:T00181 Hands-on Introduction to image analysis using Galaxy
HeLa		 Imaging Introductory 1H
GTN:T00206 Hands-on 16S Microbial Analysis with mothur (short)
microgalaxy		 Metagenomics 2h
GTN:T00338 Hands-on Taxonomic Profiling and Visualization of Metagenomic Data
metagenomicstaxonomic profilingmicrogalaxy		 Metagenomics Introductory 2H
GTN:T00201 Hands-on Analyses of metagenomics data - The global picture
microgalaxy		 Metagenomics 2H30M
GTN:T00202 Hands-on Assembly of metagenomic sequencing data
assemblymetagenomicsmicrogalaxy		 Metagenomics Introductory 2H
GTN:T00203 Hands-on Metatranscriptomics analysis using microbiome RNA-seq data
metatranscriptomicsmicrogalaxy		 Metagenomics Introductory 5H
GTN:T00208 Hands-on Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
microgalaxyNanopore data analysisPathogens detectionPhylogenetic treeHeatmapcyoa		 Metagenomics Introductory 4h
GTN:T00205 Hands-on 16S Microbial Analysis with mothur (extended)
microgalaxy		 Metagenomics 6h
GTN:T00200 Hands-on Identification of the micro-organisms in a beer using Nanopore sequencing
nanoporebeercitizen sciencemetagenomicsmicrogalaxy		 Metagenomics Introductory 1H
GTN:T00204 Hands-on Metatranscriptomics analysis using microbiome RNA-seq data (short)
metatranscriptomicsmicrogalaxy		 Metagenomics Introductory 3H
GTN:T00209 Hands-on Antibiotic resistance detection
nanoporeplasmidsassemblyamrmicrogalaxy		 Metagenomics 3h
GTN:T00207 Hands-on 16S Microbial analysis with Nanopore data
nanoporemicrogalaxy		 Metagenomics 2H
GTN:T00373 Hands-on Ploting a Microbial Genome with Circos
 Visualisation 30m
GTN:T00321 Hands-on Visualisation with Circos
 Visualisation 2h
GTN:T00322 Hands-on Genomic Data Visualisation with JBrowse
 Visualisation 1h
GTN:T00087 Hands-on Python - Files & CSV
jupyter-notebook		 Foundations of Data Science Introductory 1H30M
GTN:T00072 Hands-on Version Control with Git
 Foundations of Data Science 65M
GTN:T00081 Hands-on Advanced Python
jupyter-notebook		 Foundations of Data Science Intermediate 3H
GTN:T00082 Hands-on Python - Argparse
 Foundations of Data Science Intermediate 30M
GTN:T00098 Hands-on Python - Testing
jupyter-notebook		 Foundations of Data Science Intermediate 45M
GTN:T00110 Hands-on SQL with R
SQLRrmarkdown-notebookjupyter-notebook		 Foundations of Data Science Intermediate 45M
GTN:T00106 Hands-on Advanced SQL
SQLjupyter-notebook		 Foundations of Data Science Introductory 3H
GTN:T00092 Hands-on Python - Coding Style
jupyter-notebook		 Foundations of Data Science Intermediate 30M
GTN:T00076 Hands-on CLI basics
bashjupyter-notebook		 Foundations of Data Science Introductory 1H
GTN:T00352 Hands-on Data Manipulation Olympics - JQ
cyoajson		 Foundations of Data Science Introductory 1h
GTN:T00075 Hands-on CLI Educational Game - Bashcrawl
gamebashjupyter-notebook		 Foundations of Data Science Intermediate 2H
GTN:T00102 Hands-on Advanced R in Galaxy
R		 Foundations of Data Science Intermediate 2H
GTN:T00089 Hands-on Python - Functions
jupyter-notebook		 Foundations of Data Science Introductory 30M
GTN:T00091 Hands-on Python - Lists & Strings & Dictionaries
jupyter-notebook		 Foundations of Data Science Introductory 1H
GTN:T00078 Hands-on Data Manipulation Olympics - SQL
cyoasqljupyter-notebook		 Foundations of Data Science Introductory 1h
GTN:T00107 Hands-on Introduction to SQL
SQLjupyter-notebook		 Foundations of Data Science Introductory 3H
GTN:T00088 Hands-on Python - Flow Control
jupyter-notebook		 Foundations of Data Science Introductory 40M
GTN:T00105 Hands-on Make & Snakemake
 Foundations of Data Science Intermediate 3H
GTN:T00073 Hands-on Variant Calling Workflow
 Foundations of Data Science 50M
GTN:T00096 Hands-on Plotting in Python
jupyter-notebook		 Foundations of Data Science Intermediate 1H
GTN:T00360 Hands-on One protein along the UniProt page
 Foundations of Data Science Introductory 1H
GTN:T00079 Hands-on Basics of using Git from the Command Line
 Foundations of Data Science 30m
GTN:T00090 Hands-on Python - Globbing
jupyter-notebook		 Foundations of Data Science Intermediate 15M
GTN:T00109 Hands-on SQL with Python
SQLPythonjupyter-notebook		 Foundations of Data Science Intermediate 45M
GTN:T00353 Hands-on Data visualisation Olympics - Visualization in R
cyoaRrmarkdown-notebookjupyter-notebook		 Foundations of Data Science Introductory 1h
GTN:T00093 Hands-on Python - Loops
jupyter-notebook		 Foundations of Data Science Introductory 40M
GTN:T00085 Hands-on Conda Environments For Software Development
condajupyter-notebook		 Foundations of Data Science Intermediate 30M
GTN:T00083 Hands-on Introduction to Python
jupyter-notebook		 Foundations of Data Science Introductory 5H
GTN:T00074 Hands-on Advanced CLI in Galaxy
bashjupyter-notebook		 Foundations of Data Science Intermediate 2H
GTN:T00094 Hands-on Python - Math
jupyter-notebook		 Foundations of Data Science Introductory 30M
GTN:T00086 Hands-on Python - Try & Except
jupyter-notebook		 Foundations of Data Science Introductory 20M
GTN:T00101 Hands-on Virtual Environments For Software Development
jupyter-notebook		 Foundations of Data Science Intermediate 30M
GTN:T00099 Hands-on Python - Basic Types & Type Conversion
jupyter-notebook		 Foundations of Data Science Introductory 30M
GTN:T00100 Hands-on Python - Type annotations
jupyter-notebook		 Foundations of Data Science Intermediate 30M
GTN:T00095 Hands-on Python - Multiprocessing
jupyter-notebook		 Foundations of Data Science Advanced 30M
GTN:T00359 Hands-on Learning about one gene across biological resources and formats
 Foundations of Data Science Introductory 1H
GTN:T00104 Hands-on dplyr & tidyverse for data processing
Rrmarkdown-notebookjupyter-notebook		 Foundations of Data Science Advanced 1H
GTN:T00097 Hands-on Python - Subprocess
jupyter-notebook		 Foundations of Data Science Intermediate 45M
GTN:T00084 Hands-on Python - Introductory Graduation
jupyter-notebook		 Foundations of Data Science Introductory 1H30M
GTN:T00103 Hands-on R basics in Galaxy
interactive-toolsR		 Foundations of Data Science Introductory 3H
GTN:T00108 Hands-on SQL Educational Game - Murder Mystery
gameSQLjupyter-notebook		 Foundations of Data Science Intermediate 2H
GTN:T00054 Hands-on Protein target prediction of a bioactive ligand with Align-it and ePharmaLib
 Computational chemistry Intermediate 2H
GTN:T00053 Hands-on Setting up molecular systems
 Computational chemistry Intermediate 2H
GTN:T00049 Hands-on Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
covid19one-health		 Computational chemistry Intermediate 2H
GTN:T00050 Hands-on High Throughput Molecular Dynamics and Analysis
 Computational chemistry Advanced 3H
GTN:T00048 Hands-on Protein-ligand docking
 Computational chemistry Intermediate 3H
GTN:T00052 Hands-on Running molecular dynamics simulations using NAMD
 Computational chemistry Intermediate 3H
GTN:T00047 Hands-on Analysis of molecular dynamics simulations
 Computational chemistry Intermediate 1H
GTN:T00051 Hands-on Running molecular dynamics simulations using GROMACS
 Computational chemistry Intermediate 2H
GTN:T00114 Hands-on Data source integration
 Development in Galaxy 10M
GTN:T00117 Hands-on Creating Galaxy tools from Conda Through Deployment
 Development in Galaxy 3H
GTN:T00112 Hands-on Contributing to BioBlend as a developer
 Development in Galaxy 3h
GTN:T00116 Hands-on Galaxy Interactive Tools
 Development in Galaxy 3h
GTN:T00120 Hands-on JavaScript plugins
 Development in Galaxy 1h
GTN:T00115 Hands-on Debugging Galaxy
 Development in Galaxy 4h
GTN:T00119 Hands-on ToolFactory: Generating Tools From More Complex Scripts
 Development in Galaxy 1H
GTN:T00123 Hands-on Writing Automated Tests for Galaxy
 Development in Galaxy 3h
GTN:T00118 Hands-on ToolFactory: Generating Tools From Simple Scripts
 Development in Galaxy 1H
GTN:T00121 Hands-on Generic plugins
 Development in Galaxy 90m
GTN:T00111 Hands-on Scripting Galaxy using the API and BioBlend
jupyter-notebook		 Development in Galaxy Introductory 2h
GTN:T00113 Hands-on Contributing a New Feature to Galaxy Core
 Development in Galaxy 3H
GTN:T00122 Hands-on Galaxy Webhooks
 Development in Galaxy 1h
GTN:T00002 Hands-on Connecting Galaxy to a compute cluster
jobsansiblegit-gat		 Galaxy Server administration 1h
GTN:T00025 Hands-on Upgrading Galaxy
ansible		 Galaxy Server administration 1h
GTN:T00021 Hands-on Deploying a compute cluster in OpenStack via Terraform
terraformdeployingcloud		 Galaxy Server administration 60m
GTN:T00015 Hands-on Galaxy Monitoring with Telegraf and Grafana
ansiblemonitoringgit-gat		 Galaxy Server administration 2h
GTN:T00001 Hands-on Galaxy Installation with Ansible
ansibledeployinggit-gat		 Galaxy Server administration 2h30m
GTN:T00010 Hands-on Galaxy Interactive Tools
ansibleinteractive-tools		 Galaxy Server administration 2h
GTN:T00017 Hands-on Running Jobs on Remote Resources with Pulsar
ansiblejobsgit-gat		 Galaxy Server administration 60m
GTN:T00324 Hands-on Server Maintenance: Cleanup, Backup, and Restoration
ansibledeployinggit-gat		 Galaxy Server administration 30m
GTN:T00020 Hands-on How I learned to stop worrying and love the systemd
ansiblesystemd		 Galaxy Server administration 30m
GTN:T00011 Hands-on Automation with Jenkins
ansibleautomation		 Galaxy Server administration 1h
GTN:T00328 Hands-on Customizing the look of Galaxy (Manual)
 Galaxy Server administration 45m
GTN:T00013 Hands-on Galaxy Installation on Kubernetes
kubernetes		 Galaxy Server administration Intermediate 30m
GTN:T00325 Hands-on Deploying a Beacon v1 in Galaxy
ga4ghbeacongit-gat		 Galaxy Server administration 30m
GTN:T00330 Hands-on Monitoring Galaxy and Pulsar with Sentry
ansiblegit-gat		 Galaxy Server administration 1h
GTN:T00008 Hands-on Enable upload via FTP
datagit-gat		 Galaxy Server administration 1h
GTN:T00024 Hands-on Performant Uploads with TUS
 Galaxy Server administration 30M
GTN:T00023 Hands-on Galaxy Tool Management with Ephemeris
toolsgit-gat		 Galaxy Server administration 45m
GTN:T00022 Hands-on Training Infrastructure as a Service (TIaaS)
ansibletrainingjobsgit-gat		 Galaxy Server administration 30m
GTN:T00006 Hands-on Galaxy Database schema
 Galaxy Server administration 2h
GTN:T00018 Hands-on Galaxy Monitoring with Reports
ansiblemonitoringgit-gatbroken		 Galaxy Server administration 30m
GTN:T00005 Hands-on Data Libraries
ansiblestoragegit-gat		 Galaxy Server administration 30m
GTN:T00327 Hands-on Customizing the look of Galaxy
git-gat		 Galaxy Server administration 45m
GTN:T00000 Hands-on Ansible
ansible		 Galaxy Server administration 60m
GTN:T00326 Hands-on Setting up Celery Workers for Galaxy
ansiblegit-gat		 Galaxy Server administration 1h
GTN:T00009 Hands-on Galaxy Monitoring with gxadmin
monitoringansiblegit-gat		 Galaxy Server administration 30m
GTN:T00007 Hands-on External Authentication
authentication		 Galaxy Server administration 30m
GTN:T00004 Hands-on Reference Data with CVMFS without Ansible
 Galaxy Server administration 1h
GTN:T00003 Hands-on Reference Data with CVMFS
ansiblegit-gat		 Galaxy Server administration 1h
GTN:T00012 Hands-on Mapping Jobs to Destinations using TPV
jobsgit-gat		 Galaxy Server administration 2h
GTN:T00323 Hands-on Use Apptainer containers for running Galaxy jobs
jobsansiblegit-gat		 Galaxy Server administration 1h
GTN:T00026 Hands-on Deploying Wireguard for private mesh networking
wireguardnetworking		 Galaxy Server administration 60m
GTN:T00027 Hands-on Deploying Tailscale/Headscale for private mesh networking
wireguardnetworking		 Galaxy Server administration 60m
GTN:T00016 Hands-on Distributed Object Storage
ansiblestorage		 Galaxy Server administration 30m
GTN:T00014 Hands-on Managing Galaxy on Kubernetes
kubernetes		 Galaxy Server administration Intermediate 30m
GTN:T00329 Hands-on Reference Data with Data Managers
 Galaxy Server administration 1h
GTN:T00356 Hands-on SARS-CoV-2 Viral Sample Alignment and Variant Visualization
covid19		 Sequence analysis Introductory 1H
GTN:T00236 Hands-on Removal of human reads from SARS-CoV-2 sequencing data
covid19		 Sequence analysis Intermediate 1h
GTN:T00238 Hands-on NCBI BLAST+ against the MAdLand
 Sequence analysis 15m
GTN:T00239 Hands-on Quality Control
 Sequence analysis Introductory 1H30M
GTN:T00237 Hands-on Mapping
 Sequence analysis 1h
GTN:T00193 Hands-on IGV Introduction
 Introduction to Galaxy Analyses 2H
GTN:T00190 Hands-on A short introduction to Galaxy
español		 Introduction to Galaxy Analyses Introductory 40m
GTN:T00189 Hands-on From peaks to genes
 Introduction to Galaxy Analyses Introductory 3H
GTN:T00188 Hands-on NGS data logistics
 Introduction to Galaxy Analyses 1H30M
GTN:T00191 Hands-on Introduction to Genomics and Galaxy
 Introduction to Galaxy Analyses Introductory 2H30M
GTN:T00184 Hands-on Data Manipulation Olympics
cyoa		 Introduction to Galaxy Analyses Introductory 1h
GTN:T00187 Hands-on Galaxy 101 for everyone
 Introduction to Galaxy Analyses Introductory 1H30M
GTN:T00192 Hands-on How to reproduce published Galaxy analyses
 Introduction to Galaxy Analyses Introductory 1H
GTN:T00185 Hands-on Upload data to Galaxy
 Introduction to Galaxy Analyses Introductory 40m
GTN:T00186 Hands-on Galaxy 101
 Introduction to Galaxy Analyses Introductory 1H
GTN:T00144 Hands-on Tree thinking for tuberculosis evolution and epidemiology
prokaryoteone-healthphylogeneticsmicrogalaxy		 Evolution Introductory 1H
GTN:T00145 Hands-on Identifying tuberculosis transmission links: from SNPs to transmission clusters
prokaryoteone-healthmicrogalaxy		 Evolution Intermediate 2H
GTN:T00250 Hands-on Analysis of plant scRNA-Seq Data with Scanpy
plantspaper-replication		 Single Cell 2H
GTN:T00255 Hands-on Single-cell quality control with scater
 Single Cell 1H
GTN:T00253 Hands-on Downstream Single-cell RNA analysis with RaceID
 Single Cell 3H
GTN:T00243 Hands-on Comparing inferred cell compositions using MuSiC deconvolution
transcriptomics		 Single Cell 1H
GTN:T00256 Hands-on Understanding Barcodes
 Single Cell 2h
GTN:T00249 Hands-on Inferring single cell trajectories (Monocle3)
10xpaper-replicationR		 Single Cell 2H
GTN:T00242 Hands-on Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution
transcriptomicsdata management		 Single Cell 1H
GTN:T00254 Hands-on Clustering 3K PBMCs with Scanpy
10x		 Single Cell 5H
GTN:T00252 Hands-on Pre-processing of 10X Single-Cell RNA Datasets
10x		 Single Cell 1h
GTN:T00246 Hands-on Combining single cell datasets after pre-processing
10xpaper-replication		 Single Cell 1H
GTN:T00244 Hands-on Inferring single cell trajectories (Scanpy, Python)
10xpaper-replicationPythonjupyter-notebook		 Single Cell 2H
GTN:T00335 Hands-on Pre-processing of 10X Single-Cell ATAC-seq Datasets
10xepigenetics		 Single Cell 1h
GTN:T00248 Hands-on Removing the effects of the cell cycle
10x		 Single Cell 1H
GTN:T00251 Hands-on Pre-processing of Single-Cell RNA Data
 Single Cell 3h
GTN:T00241 Hands-on Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution
data management		 Single Cell 1H
GTN:T00336 Hands-on Inferring single cell trajectories (Monocle3, R)
10xpaper-replicationRrmarkdown-notebookjupyter-notebook		 Single Cell 3H
GTN:T00357 Hands-on Scanpy Parameter Iterator
 Single Cell 2H
GTN:T00358 Hands-on Filter, plot and explore single-cell RNA-seq data (Scanpy, Python)
10xpaper-replicationPythonjupyter-notebook		 Single Cell 3H
GTN:T00245 Hands-on Generating a single cell matrix using Alevin
10xpaper-replication		 Single Cell 2H
GTN:T00240 Hands-on Bulk RNA Deconvolution with MuSiC
transcriptomics		 Single Cell 2h
GTN:T00366 Hands-on Filter, plot, and explore single cell RNA-seq data (Seurat, R)
10xpaper-replicationRrmarkdown-notebookjupyter-notebook		 Single Cell 3H
GTN:T00247 Hands-on Filter, plot and explore single-cell RNA-seq data (Scanpy)
10xpaper-replication		 Single Cell 3H
GTN:T00374 Hands-on EBI Single Cell Expression Atlas files to AnnData (Scanpy) or Seurat Object | Creating preprocessed dataset for sc-RNA Filter, Plot, Explore tutorial
data importdata management		 Single Cell 15m
GTN:T00371 Hands-on Asynchronous training
 Teaching and Hosting Galaxy training 1h
GTN:T00283 Hands-on Organizing a workshop
 Teaching and Hosting Galaxy training 3H
GTN:T00284 Hands-on Running a workshop as instructor
 Teaching and Hosting Galaxy training 3H
GTN:T00282 Hands-on Motivation and Demotivation
 Teaching and Hosting Galaxy training 60m
GTN:T00287 Hands-on Teaching online
 Teaching and Hosting Galaxy training 1h
GTN:T00285 Hands-on Set up a Galaxy for Training
 Teaching and Hosting Galaxy training 2h
GTN:T00286 Hands-on Training Infrastructure as a Service
cyoa		 Teaching and Hosting Galaxy training 10m
GTN:T00279 Hands-on Hybrid training
 Teaching and Hosting Galaxy training 1h
GTN:T00281 Hands-on Live Coding is a Skill
 Teaching and Hosting Galaxy training 1h
GTN:T00372 Hands-on Course Builder
cyoa		 Teaching and Hosting Galaxy training 10m
GTN:T00354 Hands-on Train-the-Trainer: putting it all together
 Teaching and Hosting Galaxy training 60m
GTN:T00280 Hands-on Training techniques to enhance learner participation and engagement
 Teaching and Hosting Galaxy training 60m
GTN:T00277 Hands-on Teaching experiences
 Teaching and Hosting Galaxy training 1h
GTN:T00276 Hands-on Assessment and feedback in training and teachings
 Teaching and Hosting Galaxy training 3h30m
GTN:T00278 Hands-on Galaxy Admin Training
 Teaching and Hosting Galaxy training 60m
GTN:T00030 Hands-on Chloroplast genome assembly
plantsnanopore		 Assembly 2h
GTN:T00038 Hands-on Unicycler Assembly
prokaryotemicrogalaxy		 Assembly Introductory 4h
GTN:T00039 Hands-on VGP assembly pipeline
pacbioeukaryoteVGP		 Assembly Intermediate 5h
GTN:T00036 Hands-on Genome Assembly of MRSA using Illumina MiSeq Data
illuminaassemblyamrone-health		 Assembly 2h
GTN:T00029 Hands-on Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
covid19		 Assembly Intermediate 4h
GTN:T00331 Hands-on Large genome assembly and polishing
assemblypolishingnanopore		 Assembly 2h
GTN:T00037 Hands-on Genome Assembly of MRSA using Oxford Nanopore MinION Data
nanoporeassemblyamr		 Assembly 2h
GTN:T00032 Hands-on Making sense of a newly assembled genome
prokaryotemicrogalaxy		 Assembly 4h
GTN:T00035 Hands-on Assembly of metagenomic sequencing data
assemblymetagenomicsmicrogalaxy		 Assembly Introductory 2H
GTN:T00355 Hands-on ERGA post-assembly QC
 Assembly 3H
GTN:T00031 Hands-on De Bruijn Graph Assembly
 Assembly Introductory 2h
GTN:T00034 Hands-on An Introduction to Genome Assembly
 Assembly Introductory 30m
GTN:T00040 Hands-on VGP assembly pipeline - short version
pacbioeukaryoteVGP		 Assembly Intermediate 1h
GTN:T00028 Hands-on Genome Assembly Quality Control
assemblyquality control		 Assembly Intermediate 2h
GTN:T00033 Hands-on Genome assembly using PacBio data
assemblypacbio		 Assembly Intermediate 6h
GTN:T00293 Hands-on Network analysis with Heinz
metatranscriptomicsnetwork analysis		 Transcriptomics 1h30m
GTN:T00289 Hands-on De novo transcriptome reconstruction with RNA-Seq
 Transcriptomics 6h
GTN:T00303 Hands-on Visualization of RNA-Seq results with heatmap2
 Transcriptomics 1h
GTN:T00291 Hands-on GO Enrichment Analysis
 Transcriptomics 1h
GTN:T00304 Hands-on Visualization of RNA-Seq results with Volcano Plot
 Transcriptomics Introductory 30m
GTN:T00302 Hands-on Visualization of RNA-Seq results with CummeRbund
 Transcriptomics 1h
GTN:T00306 Hands-on Small Non-coding RNA Clustering using BlockClust
 Transcriptomics 1H
GTN:T00299 Hands-on RNA Seq Counts to Viz in R
interactive-tools		 Transcriptomics 1H
GTN:T00345 Hands-on Genome-wide alternative splicing analysis
alternative splicingisoform switching		 Transcriptomics Advanced 3H
GTN:T00307 Hands-on Differential abundance testing of small RNAs
 Transcriptomics 3h
GTN:T00305 Hands-on Visualization of RNA-Seq results with Volcano Plot in R
interactive-tools		 Transcriptomics Intermediate 1H
GTN:T00300 Hands-on 3: RNA-seq genes to pathways
mouse		 Transcriptomics 2h
GTN:T00294 Hands-on Reference-based RNAseq data analysis (long)
 Transcriptomics 1h
GTN:T00292 Hands-on Whole transcriptome analysis of Arabidopsis thaliana
miRNAplantsstress tolerance		 Transcriptomics 2H
GTN:T00297 Hands-on RNA-Seq analysis with AskOmics Interactive Tool
 Transcriptomics 2H
GTN:T00290 Hands-on De novo transcriptome assembly, annotation, and differential expression analysis
 Transcriptomics 3H
GTN:T00298 Hands-on 2: RNA-seq counts to genes
limma-voommouseQC		 Transcriptomics 2h
GTN:T00295 Hands-on Reference-based RNA-Seq data analysis
bulkrna-seqcollectionsdrosophilaQCcyoa		 Transcriptomics Introductory 8h
GTN:T00301 Hands-on 1: RNA-Seq reads to counts
collectionsmouseQC		 Transcriptomics 3h
GTN:T00296 Hands-on RNA-RNA interactome data analysis
 Transcriptomics 2H
GTN:T00288 Hands-on CLIP-Seq data analysis from pre-processing to motif detection
 Transcriptomics 6h
GTN:T00346 Hands-on RNA-seq Alignment with STAR
 Transcriptomics 90M
GTN:T00153 Hands-on JupyterLab in Galaxy
interactive-tools		 Using Galaxy and Managing your Data 1H
GTN:T00147 Hands-on Downloading and Deleting Data in Galaxy
 Using Galaxy and Managing your Data Introductory 20M
GTN:T00159 Hands-on Submitting sequence data to ENA
covid19		 Using Galaxy and Managing your Data Intermediate 1h
GTN:T00148 Hands-on Use Jupyter notebooks in Galaxy
 Using Galaxy and Managing your Data 30m
GTN:T00156 Hands-on Multisample Analysis
collections		 Using Galaxy and Managing your Data Advanced 1h
GTN:T00160 Hands-on Rule Based Uploader
collectionstags		 Using Galaxy and Managing your Data Intermediate 20m
GTN:T00151 Hands-on Extracting Workflows from Histories
workflows		 Using Galaxy and Managing your Data 30m
GTN:T00164 Hands-on Using Workflow Parameters
workflows		 Using Galaxy and Managing your Data Intermediate 30m
GTN:T00158 Hands-on Searching Your History
 Using Galaxy and Managing your Data Introductory 5m
GTN:T00149 Hands-on Group tags for complex experimental designs
 Using Galaxy and Managing your Data 10m
GTN:T00150 Hands-on Understanding Galaxy history system
 Using Galaxy and Managing your Data 30m
GTN:T00152 Hands-on InterMine integration with Galaxy
 Using Galaxy and Managing your Data 1h
GTN:T00162 Hands-on Automating Galaxy workflows using the command line
workflowsvariant-analysiscovid19		 Using Galaxy and Managing your Data 2h
GTN:T00165 Hands-on Workflow Reports
workflows		 Using Galaxy and Managing your Data Intermediate 30m
GTN:T00146 Hands-on Using dataset collections
collections		 Using Galaxy and Managing your Data Intermediate 30m
GTN:T00157 Hands-on RStudio in Galaxy
interactive-tools		 Using Galaxy and Managing your Data 3H
GTN:T00161 Hands-on Rule Based Uploader: Advanced
collectionstags		 Using Galaxy and Managing your Data Advanced 20m
GTN:T00155 Hands-on SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis
ncbicovid19		 Using Galaxy and Managing your Data 30m
GTN:T00163 Hands-on Creating, Editing and Importing Galaxy Workflows
workflows		 Using Galaxy and Managing your Data Intermediate 30m
GTN:T00154 Hands-on Name tags for following complex histories
 Using Galaxy and Managing your Data 20m
GTN:T00258 Hands-on Deep Learning (Part 1) - Feedforward neural networks (FNN)
 Statistics and machine learning 2H
GTN:T00260 Hands-on PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
Machine learningPan-cancercancer biomarkersoncogenes and tumor suppressor genes		 Statistics and machine learning 1H30M
GTN:T00259 Hands-on Deep Learning (Part 2) - Recurrent neural networks (RNN)
 Statistics and machine learning 2H
GTN:T00268 Hands-on Introduction to deep learning
 Statistics and machine learning 1H
GTN:T00271 Hands-on Regression in Machine Learning
 Statistics and machine learning 2H
GTN:T00337 Hands-on Supervised Learning with Hyperdimensional Computing
 Statistics and machine learning Intermediate 30m
GTN:T00257 Hands-on Deep Learning (Part 3) - Convolutional neural networks (CNN)
 Statistics and machine learning 2H
GTN:T00266 Hands-on A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy
interactive-toolsmachine-learningdeep-learningjupyter-labimage-segmentationprotein-3D-structure		 Statistics and machine learning 1H
GTN:T00262 Hands-on Classification in Machine Learning
 Statistics and machine learning 2H
GTN:T00263 Hands-on Machine learning: classification and regression
 Statistics and machine learning 1H
GTN:T00269 Hands-on Interval-Wise Testing for omics data
 Statistics and machine learning 1h
GTN:T00272 Hands-on Text-mining with the SimText toolset
interactive-tools		 Statistics and machine learning 1H
GTN:T00264 Hands-on Clustering in Machine Learning
 Statistics and machine learning 2H
GTN:T00265 Hands-on Image classification in Galaxy with fruit 360 dataset
 Statistics and machine learning 2H
GTN:T00267 Hands-on Introduction to Machine Learning using R
interactive-tools		 Statistics and machine learning Intermediate 3H
GTN:T00270 Hands-on Basics of machine learning
 Statistics and machine learning 30M
GTN:T00261 Hands-on Age prediction using machine learning
 Statistics and machine learning 2H
GTN:T00167 Hands-on Genome annotation with Maker (short)
eukaryote		 Genome Annotation Intermediate 2h
GTN:T00173 Hands-on Functional annotation of protein sequences
eukaryote		 Genome Annotation Introductory 1h
GTN:T00176 Hands-on From small to large-scale genome comparison
 Genome Annotation 2H
GTN:T00172 Hands-on Genome annotation with Funannotate
eukaryote		 Genome Annotation Intermediate 8h
GTN:T00169 Hands-on Refining Genome Annotations with Apollo (prokaryotes)
prokaryotemicrogalaxy		 Genome Annotation Intermediate 3h
GTN:T00178 Hands-on Masking repeats with RepeatMasker
eukaryote		 Genome Annotation Introductory 1H
GTN:T00171 Hands-on CRISPR screen analysis
genome editingCRISPRessential genescell line		 Genome Annotation 2H
GTN:T00179 Hands-on Essential genes detection with Transposon insertion sequencing
bacteriatnseqessential genes		 Genome Annotation 7H
GTN:T00168 Hands-on Genome annotation with Prokka
prokaryotemicrogalaxy		 Genome Annotation Introductory 1h
GTN:T00170 Hands-on Refining Genome Annotations with Apollo (eukaryotes)
eukaryotecyoa		 Genome Annotation Intermediate 3h
GTN:T00177 Hands-on Long non-coding RNAs (lncRNAs) annotation with FEELnc
eukaryote		 Genome Annotation Intermediate 2h
GTN:T00370 Hands-on Creating an Official Gene Set
 Genome Annotation 30M
GTN:T00175 Hands-on Genome Annotation
prokaryotework-in-progress		 Genome Annotation Introductory 2H
GTN:T00174 Hands-on Comparative gene analysis in unannotated genomes
evolutionannotationvgpcookbookeukaryoteprokaryotemicrogalaxy		 Genome Annotation 30M
GTN:T00166 Hands-on Genome annotation with Maker
eukaryote		 Genome Annotation Advanced 4h
GTN:T00198 Hands-on Mass spectrometry imaging: Examining the spatial distribution of analytes
 Metabolomics Introductory 1H
GTN:T00199 Hands-on Mass spectrometry imaging: Finding differential analytes
 Metabolomics Intermediate 2H
GTN:T00194 Hands-on Mass spectrometry : GC-MS analysis with metaMS package
 Metabolomics Introductory 2H
GTN:T00196 Hands-on Mass spectrometry: LC-MS data processing
 Metabolomics Introductory 2H
GTN:T00197 Hands-on Mass spectrometry: LC-MS preprocessing with XCMS
 Metabolomics Intermediate 3h
GTN:T00195 Hands-on Mass spectrometry: LC-MS analysis
 Metabolomics 3h
GTN:T00344 Hands-on Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
 Metabolomics Intermediate 2H
GTN:F00240 FAQs How can I create a tutorial skeleton from a Galaxy workflow?
 Contributing to the Galaxy Training Material
GTN:F00110 FAQs Using tutorial mode
GTN:F00220 FAQs I got slightly different numbers than were in the tutorial
 Introduction to Galaxy Analyses
GTN:F00258 FAQs UCSC import: what should my file look like?
 Epigenetics
GTN:F00326 FAQs The UMAP Plots errors out sometimes?
 Single Cell
GTN:F00229 FAQs Are UMIs not actually unique?
 Single Cell
GTN:F00235 FAQs Downloading the files from the NCBI server fails or takes too long.
 Assembly
GTN:F00354 FAQs How can I talk with other users?
 Single Cell
GTN:F00111 FAQs Does your account usage quota seem incorrect?
GTN:F00112 FAQs Forgot Password
GTN:F00113 FAQs Changing acount email or password
GTN:F00230 FAQs Why do we only consider highly variable genes?
 Single Cell
GTN:F00347 FAQs Can we use snippy pipeline instead for the phylogenetic analysis?
 Metagenomics
GTN:F00312 FAQs Why do we have a variant mapping file when it is not being used in the workflow?
 Proteomics
GTN:F00114 FAQs Using IGV with Galaxy
GTN:F00231 FAQs Add genome and annotations to IGV from Galaxy
 Visualisation
GTN:F00232 FAQs Add Mapped reads track to IGV from Galaxy
 Visualisation
GTN:F00270 FAQs Why don't we perform the V-Search dereplication step of ASaiM for metatrascriptomic data?
 Metagenomics
GTN:F00356 FAQs What is a Learning Pathway?
GTN:F00181 FAQs Why host your materials with the GTN?
GTN:F00115 FAQs Why not use Excel?
GTN:F00281 FAQs Can EncyclopeDIA be run on a DIA-MS dataset without a spectral library?
 Proteomics
GTN:F00348 FAQs Can we also use this workflow on Illumina raw reads?
 Metagenomics
GTN:F00349 FAQs Do the pipelines work with both isolates and direct from raw meat? or only isolate?
 Metagenomics
GTN:F00116 FAQs Annotate a workflow
GTN:F00117 FAQs Creating a new workflow
GTN:F00118 FAQs Opening the workflow editor
GTN:F00119 FAQs Extracting a workflow from your history
GTN:F00136 FAQs Extraer un flujo de trabajo de tu historial
GTN:F00120 FAQs Hiding intermediate steps
GTN:F00121 FAQs Importing a workflow
GTN:F00175 FAQs Import workflows from WorkflowHub
GTN:F00122 FAQs Importing a workflow using the search
GTN:F00123 FAQs Setting parameters at run-time
GTN:F00124 FAQs Make a workflow public
GTN:F00125 FAQs Renaming workflow outputs
GTN:F00126 FAQs Viewing a workflow report
GTN:F00127 FAQs Running a workflow
GTN:F00176 FAQs Importing and Launching a workflow